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- PDB-4xa9: Crystal structure of the complex between the N-terminal domain of... -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 4xa9
タイトルCrystal structure of the complex between the N-terminal domain of RavJ and LegL1 from Legionella pneumophila str. Philadelphia
要素
  • Gala protein type 1, 3 or 4
  • Uncharacterized protein
キーワードStructural genomics / Unknown Function / infection / effector / papain-like cysteine protease family / leucine-rich-repeat / complex / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
機能・相同性Domain of unknown function DUF5617 / Domain of unknown function (DUF5617) / Leucine Rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Gala protein type 1, 3 or 4 / DUF5617 domain-containing protein
機能・相同性情報
生物種Legionella pneumophila subsp. pneumophila (バクテリア)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2 Å
データ登録者Stogios, P.J. / Cuff, M.E. / Nocek, B. / Evdokimova, E. / Di Leo, R. / Yim, V. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
資金援助 米国, 2件
組織認可番号
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 米国
Department of Energy (DOE, United States)AC02-06CH11357 米国
引用ジャーナル: Mol. Syst. Biol. / : 2016
タイトル: Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila.
著者: Urbanus, M.L. / Quaile, A.T. / Stogios, P.J. / Morar, M. / Rao, C. / Di Leo, R. / Evdokimova, E. / Lam, M. / Oatway, C. / Cuff, M.E. / Osipiuk, J. / Michalska, K. / Nocek, B.P. / Taipale, M. ...著者: Urbanus, M.L. / Quaile, A.T. / Stogios, P.J. / Morar, M. / Rao, C. / Di Leo, R. / Evdokimova, E. / Lam, M. / Oatway, C. / Cuff, M.E. / Osipiuk, J. / Michalska, K. / Nocek, B.P. / Taipale, M. / Savchenko, A. / Ensminger, A.W.
履歴
登録2014年12月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年1月28日Provider: repository / タイプ: Initial release
改定 1.12017年1月4日Group: Database references
改定 1.22017年9月20日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32019年12月4日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Gala protein type 1, 3 or 4
a: Uncharacterized protein
B: Gala protein type 1, 3 or 4
b: Uncharacterized protein
C: Gala protein type 1, 3 or 4
c: Uncharacterized protein
D: Gala protein type 1, 3 or 4
d: Uncharacterized protein
E: Gala protein type 1, 3 or 4
e: Uncharacterized protein
F: Gala protein type 1, 3 or 4
f: Uncharacterized protein
G: Gala protein type 1, 3 or 4
g: Uncharacterized protein
H: Gala protein type 1, 3 or 4
h: Uncharacterized protein


分子量 (理論値)分子数
合計 (水以外)465,11316
ポリマ-465,11316
非ポリマー00
81,2844512
1
A: Gala protein type 1, 3 or 4
a: Uncharacterized protein


分子量 (理論値)分子数
合計 (水以外)58,1392
ポリマ-58,1392
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-12 kcal/mol
Surface area19590 Å2
手法PISA
2
B: Gala protein type 1, 3 or 4
b: Uncharacterized protein


分子量 (理論値)分子数
合計 (水以外)58,1392
ポリマ-58,1392
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-11 kcal/mol
Surface area19400 Å2
手法PISA
3
C: Gala protein type 1, 3 or 4
c: Uncharacterized protein


分子量 (理論値)分子数
合計 (水以外)58,1392
ポリマ-58,1392
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-13 kcal/mol
Surface area19250 Å2
手法PISA
4
D: Gala protein type 1, 3 or 4
d: Uncharacterized protein


分子量 (理論値)分子数
合計 (水以外)58,1392
ポリマ-58,1392
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-12 kcal/mol
Surface area19860 Å2
手法PISA
5
E: Gala protein type 1, 3 or 4
e: Uncharacterized protein


分子量 (理論値)分子数
合計 (水以外)58,1392
ポリマ-58,1392
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-12 kcal/mol
Surface area19460 Å2
手法PISA
6
F: Gala protein type 1, 3 or 4
f: Uncharacterized protein


分子量 (理論値)分子数
合計 (水以外)58,1392
ポリマ-58,1392
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-10 kcal/mol
Surface area19770 Å2
手法PISA
7
G: Gala protein type 1, 3 or 4
g: Uncharacterized protein


分子量 (理論値)分子数
合計 (水以外)58,1392
ポリマ-58,1392
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-11 kcal/mol
Surface area19550 Å2
手法PISA
8
H: Gala protein type 1, 3 or 4
h: Uncharacterized protein


分子量 (理論値)分子数
合計 (水以外)58,1392
ポリマ-58,1392
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-10 kcal/mol
Surface area19360 Å2
手法PISA
単位格子
Length a, b, c (Å)219.608, 120.885, 149.288
Angle α, β, γ (deg.)90.00, 92.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11A-303-

HOH

21E-302-

HOH

31E-332-

HOH

41E-337-

HOH

51e-301-

HOH

61e-307-

HOH

71h-329-

HOH

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要素

#1: タンパク質
Gala protein type 1, 3 or 4


分子量: 32378.555 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Legionella pneumophila subsp. pneumophila (バクテリア)
: Philadelphia 1 / ATCC 33152 / DSM 7513 / 遺伝子: legL1, lpg0945 / プラスミド: p15Tv lic / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q5ZWY8
#2: タンパク質
Uncharacterized protein


分子量: 25760.525 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Legionella pneumophila subsp. pneumophila (バクテリア)
: Philadelphia 1 / ATCC 33152 / DSM 7513 / 遺伝子: lpg0944 / プラスミド: p15Tv lic / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q5ZWY9
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 4512 / 由来タイプ: 天然 / : H2O

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 2.13 Å3/Da / 溶媒含有率: 42.27 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 0.1 M NaCl, 100 mM Tris pH 8.5 and 26% (w/v) PEG3350

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.97924 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年11月7日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97924 Å / 相対比: 1
反射解像度: 2→30 Å / Num. obs: 258259 / % possible obs: 97.8 % / 冗長度: 3.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.14
反射 シェル解像度: 2→2.03 Å / 冗長度: 2.9 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.82 / % possible all: 94.4

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.9_1692)精密化
HKL-3000データ削減
HKL-3000データスケーリング
SHELX位相決定
ARPモデル構築
Cootモデル構築
精密化構造決定の手法: 単波長異常分散 / 解像度: 2→29.943 Å / SU ML: 0.18 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 19.71 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.1946 22498 5.01 %Random selection
Rwork0.1577 ---
obs0.1595 256033 86.64 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2→29.943 Å
タンパク質核酸リガンド溶媒全体
原子数29186 0 0 4512 33698
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00630160
X-RAY DIFFRACTIONf_angle_d0.85441123
X-RAY DIFFRACTIONf_dihedral_angle_d12.7811237
X-RAY DIFFRACTIONf_chiral_restr0.0454800
X-RAY DIFFRACTIONf_plane_restr0.0045382
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.23624570.19748827X-RAY DIFFRACTION53
2.0227-2.04650.24384640.19359385X-RAY DIFFRACTION57
2.0465-2.07150.23615330.18110030X-RAY DIFFRACTION61
2.0715-2.09770.21235530.176310790X-RAY DIFFRACTION66
2.0977-2.12530.21316380.16911534X-RAY DIFFRACTION70
2.1253-2.15440.20296020.170511917X-RAY DIFFRACTION72
2.1544-2.18520.22946590.16812384X-RAY DIFFRACTION76
2.1852-2.21780.20426690.173412767X-RAY DIFFRACTION78
2.2178-2.25240.21327050.165813470X-RAY DIFFRACTION81
2.2524-2.28930.23326910.165813856X-RAY DIFFRACTION84
2.2893-2.32880.21317930.163614362X-RAY DIFFRACTION88
2.3288-2.37110.20367240.161914900X-RAY DIFFRACTION90
2.3711-2.41670.21098380.165315263X-RAY DIFFRACTION93
2.4167-2.4660.19948030.166615660X-RAY DIFFRACTION95
2.466-2.51960.22728220.164815736X-RAY DIFFRACTION96
2.5196-2.57820.21698700.166215745X-RAY DIFFRACTION97
2.5782-2.64260.20317880.165215993X-RAY DIFFRACTION97
2.6426-2.7140.20578700.165816121X-RAY DIFFRACTION98
2.714-2.79380.21578970.173616045X-RAY DIFFRACTION98
2.7938-2.88390.22598460.174215928X-RAY DIFFRACTION98
2.8839-2.98690.20788190.165316078X-RAY DIFFRACTION97
2.9869-3.10640.20618390.167915931X-RAY DIFFRACTION97
3.1064-3.24760.20348500.160215860X-RAY DIFFRACTION97
3.2476-3.41860.18568580.154615881X-RAY DIFFRACTION97
3.4186-3.63240.17548510.141815711X-RAY DIFFRACTION96
3.6324-3.91240.16628220.134215672X-RAY DIFFRACTION95
3.9124-4.3050.15688160.132215510X-RAY DIFFRACTION95
4.305-4.92560.16898430.137215367X-RAY DIFFRACTION94
4.9256-6.19670.17897970.153715324X-RAY DIFFRACTION93
6.1967-29.94590.1797810.166614540X-RAY DIFFRACTION89
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.00060.0005-0.00270.00460.00120.0010.0219-0.0127-0.00130.0351-0.0121-0.01160.00330.018500.14540.05240.0190.19530.04220.2185119.320591.822668.7731
20.0164-0.0181-0.00120.0148-0.0060.01350.06150.0646-0.0358-0.1291-0.1295-0.03920.06880.0125-0.02140.180.0580.00040.13180.00270.1598110.546186.75759.7858
30.0524-0.0237-0.01520.0337-0.02240.04560.05750.1119-0.1346-0.1069-0.02310.18820.0285-0.0590.01070.14380.0498-0.05180.1287-0.03690.215288.841795.43355.7242
40.00650.00320.0010.0063-0.00050.0166-0.0209-0.0137-0.0365-0.0092-0.02630.0709-0.0037-0.0083-0.00080.10370.0543-0.00650.18430.01440.258978.0474109.315963.0977
50.0018-0.00140.00120.00200.00190.0283-0.01820.0133-0.01650.009-0.0043-0.0252-0.012900.17820.04590.03240.23060.02490.270883.006112.956765.8004
60.00150.0007-0.00130.0004-0.00250.00170.0322-0.00920.0005-0.0516-0.00250.02120.0047-0.011500.1938-0.05880.05550.19270.03780.2967154.7909122.66885.6151
70.01150.0034-0.00150.0030.00150.0024-0.0274-0.00680.00140.01910.00240.0045-0.0061-0.0447-0.00430.1734-0.03740.05390.16050.04390.3084156.2293120.985216.4905
80.03330.0152-0.00790.0125-0.00860.01960.0316-0.0416-0.1110.0491-0.01170.03010.075-0.06040.01290.162-0.04010.05650.12410.01820.1775165.9366117.171515.0436
90.01030.0006-0.01030.0295-0.01190.01590.0044-0.1024-0.17940.0538-0.0497-0.1865-0.00180.1013-0.00720.1196-0.03810.02030.14790.0190.1864187.4256128.212616.6306
100.009-0.0012-0.01110.00730.00130.0092-0.01180.0230.0056-0.0042-0.0389-0.0101-0.0072-0.0058-0.00060.1679-0.05520.04360.17480.00160.2121193.0433145.32979.2654
110.0216-0.03020.00090.0501-0.00440.00150.01320.0274-0.0392-0.0456-0.0561-0.03540.0005-0.01810.00040.1778-0.10450.0330.2983-0.02010.1316137.893248.31177.0523
120.06020.02080.00820.0475-0.02790.0301-0.0498-0.03780.11720.03060.05170.0063-0.18570.09330.00260.147-0.06870.00410.112-0.00090.1044125.101453.149515.5008
130.03030.0060.02290.02610.00360.01560.0151-0.04090.10740.02870.01370.1484-0.0139-0.12190.00880.0983-0.021-0.00250.1850.02360.1338102.512340.854415.9142
140.00730.00030.00390.0046-0.00080.00450.0030.0343-0.0316-0.0372-0.03610.0144-0.01340.0012-0.00050.1428-0.0709-0.03220.23630.02950.122898.007926.58248.8973
150.00150.000900.0028-0.00170.0005-0.00670.002-0.00330.0151-0.00690.00230.00880.001-00.1342-0.025-0.03140.16570.02230.1905103.585721.020616.0615
160.0020.003-0.00040.0044-0.00030.00040.04150.01570.0191-0.0345-0.02760.01370.0057-0.0341-00.1881-0.03530.05080.2085-0.03050.2856151.087562.55195.4985
170.02910.0133-0.00860.02430.00250.02610.0847-0.0352-0.09380.1726-0.1014-0.01910.1809-0.08870.00620.1838-0.06080.0360.14-0.00240.1605160.964358.217915.9886
180.01130.0060.00060.0114-0.01380.01440.0307-0.0476-0.07560.0941-0.0112-0.06710.07670.140600.1502-0.0039-0.01920.15420.01650.2262181.98564.471819.5288
190.0151-0.0017-0.00170.0089-0.00880.0134-0.03410.0166-0.02250.0192-0.0523-0.09210.01610.0592-0.00520.1366-0.0534-0.00020.2068-0.0170.2279191.08276.979412.686
200.00260.00080.00150.00130.0010.00160.04460.05170.02240.00730.00510.0150.00660.029500.1685-0.05120.02370.1946-0.01610.255187.468382.96049.4727
210.0190.0218-0.00770.026-0.00710.0001-0.09210.12540.1198-0.01320.0473-0.057-0.04520.1149-0.00810.0348-0.1752-0.02310.11240.08990.2683136.9015111.699411.6807
220.0019-0.0001-0.00180.00030.00020.00170.0305-0.02130.02810.0097-0.0031-0.0039-0.01420.00050.00450.2335-0.0203-0.05770.1152-0.09270.3672125.0696118.005821.5359
230.0166-0.00140.01280.0094-0.00320.0119-0.04780.02010.16650.0282-0.02070.02930.0121-0.0011-0.00140.1309-0.0156-0.03520.08190.00510.2131120.1412112.635116.3963
240.0631-0.01670.04710.04060.02570.0935-0.0264-0.08750.16880.0758-0.05190.0407-0.0098-0.1666-0.05070.07150.00940.00110.1198-0.04090.1187105.4653102.576815.4727
250.0079-0.00330.00160.00540.00090.00420.03960.0526-0.0257-0.0004-0.04710.01630.0094-0.03770.00010.097-0.031-0.00180.1495-0.00580.1173101.965487.42899.5813
260.00090-0.00130.0002-0.00170.00750.00630.00220.0005-0.0039-0.00280.01620.0014000.16690.0751-0.03690.3038-0.05810.2577126.700579.250960.7958
270.0011-0.0002-0.00120.0004-0.00110.00250.0013-0.03-0.01090.02-0.0070.01650.01760.0221-00.1870.05410.00040.47210.08870.235134.30175.507172.4147
280.1385-0.10680.03330.0715-0.02590.03250.03550.00110.3256-0.0833-0.0263-0.0742-0.0721-0.0294-0.03380.15860.0788-0.01550.1588-0.03750.1811147.773481.546558.9472
290.0307-0.0108-0.0020.0159-0.01540.01390.08270.06220.1507-0.0798-0.0932-0.1206-0.00950.0432-0.00670.12170.0349-0.00030.1871-0.00850.1402170.382468.588260.0722
300.00580.00240.00870.0084-0.00260.0115-0.0138-0.0472-0.04330.0119-0.06050.01480.0126-0.0101-0.00460.12470.0398-0.04190.21-0.00820.1643171.42155.780864.1259
310.0026-0.0029-0.00290.00250.00150.0033-0.007-0.0439-0.02350.0118-0.05830.0458-0.0020.0199-00.21570.09390.03870.42170.06160.3973133.2298138.53368.72
320.0764-0.06940.01660.0729-0.00170.0580.00090.01620.0577-0.14930.0185-0.013-0.2858-0.10770.06280.0630.183-0.05230.0725-0.02520.1469148.5182143.136658.5221
330.0151-0.01050.01610.0166-0.0190.0261-0.00570.11710.0484-0.0278-0.0716-0.0935-0.03330.0513-0.02170.10240.02410.00310.1176-0.00730.1097169.5098133.113756.9467
340.0081-0.00690.00480.0058-0.00140.00110.0256-0.0287-0.0099-0.0181-0.0474-0.031-0.01380.0115-0.00330.07620.0433-0.01350.1756-0.03130.1109174.2557124.711660.6712
350.00720.00350.00450.00550.00210.0016-0.007-0.0242-0.07320.0491-0.0446-0.0293-0.00370.0311-0.00530.08780.0317-0.02450.125-0.03080.1619172.537116.890662.4505
360.00150.0004-0.00040.00020.00090.00190.0288-0.0273-0.00150.010.00690.003-0.0020.0025-00.23550.0694-0.01430.2966-0.00560.3072124.42831.89665.0469
370.01910.01860.00440.0320.0050.0030.0876-0.0166-0.08640.108-0.0555-0.00790.03960.0085-0.00410.16490.07640.00570.18780.00450.2448116.088829.098366.318
380.069-0.0202-0.01110.08050.02910.07830.0920.1572-0.1475-0.0335-0.11720.08960.1771-0.0065-0.02620.0860.22090.0522-0.1005-0.17730.1841101.411429.481155.1835
390.0187-0.00380.00590.0115-0.00830.0160.04510.0779-0.1424-0.082-0.03610.16220.032-0.10510.00540.15590.0613-0.02640.1927-0.03580.254382.705741.937557.3642
400.005-0.0049-0.00070.00710.0007-0.0009-0.0144-0.0330.02420.0329-0.00410.02170.0247-0.0268-0.0010.11020.0709-0.0020.1899-0.02690.279581.080554.205163.0738
410.0662-0.04790.06580.0712-0.0610.06950.1182-0.0347-0.0057-0.03240.1033-0.0304-0.07070.06720.1080.177-0.02980.08470.2435-0.1480.1673110.108116.585160.1319
420.0080.0050.0040.00380.00620.01090.0065-0.02570.0457-0.02140.00810.0402-0.06340.0647-00.18610.00430.01680.30360.0030.196196.4351117.028767.2472
430.0405-0.01130.05940.0103-0.01760.0970.1086-0.07180.0625-0.05080.0941-0.0949-0.0405-0.04630.06070.3247-0.00380.18910.1649-0.06560.3282103.5777125.35656.8665
440.0318-0.05030.06880.1117-0.13260.17030.1364-0.01140.0503-0.08840.103-0.0501-0.0416-0.02160.06380.25270.02930.10250.1507-0.04310.2063107.5093115.271844.2194
450.1982-0.03010.14930.0754-0.06430.18430.2279-0.07330.079-0.12090.1356-0.0371-0.14750.14090.17840.2280.01950.1470.1885-0.06810.2104110.256115.996548.6382
460.04840.03250.04550.0550.05950.06940.06020.05610.0130.03040.08960.0851-0.0778-0.0740.07140.16890.02480.07260.170.08770.2178163.9854146.897415.0965
470.0061-0.00570.01110.0051-0.01220.01160.058-0.00480.03090.04150.058-0.0133-0.0614-0.0678-00.1983-0.02660.04210.2616-0.00240.1971176.5226148.41987.7424
480.0857-0.00870.06150.0025-0.00710.05060.09310.10870.12260.087-0.02410.09060.00460.06360.05620.32990.02180.17130.16620.0840.3014170.3297156.125318.371
490.00560.01020.01310.02510.02630.03580.0490.00080.07230.07470.03640.0927-0.0450.00590.03470.27730.02410.16260.15090.0260.1935165.8289146.3430.8286
500.0612-0.01950.02050.01590.00150.02410.07330.05110.10170.17290.02570.2215-0.0825-0.04810.00850.2677-0.00480.1340.15490.04470.2734163.8885146.649627.0141
510.03880.0619-0.04810.0945-0.07510.05830.06630.04070.0112-0.00650.1049-0.02660.06070.13470.08030.12750.0615-0.05180.1886-0.08440.1069127.943425.377516.6673
520.0198-0.0181-0.02750.05990.03770.06130.1237-0.0122-0.1362-0.03750.06450.04280.08040.08040.09340.21710.0603-0.13570.276-0.01950.0677115.317721.87389.8701
530.0257-0.0235-0.00470.0113-0.00330.00620.11320.0725-0.1501-0.01910.0008-0.01440.0769-0.00640.05650.1710.2091-0.4496-0.06040.14050.0249121.89215.955121.7319
540.02640.0265-0.03130.051-0.06450.09220.087-0.0414-0.06130.11010.0508-0.01180.04170.02390.07460.17790.032-0.08080.24530.0040.0651125.678427.32534.4761
550.1736-0.015-0.00560.0321-0.03370.11670.19050.0405-0.16520.10320.0217-0.11470.1850.20680.24440.20990.0187-0.09830.2109-0.02140.1577128.772926.3828.3445
560.00780.01010.00340.01060.00540.00270.03720.0697-0.01110.032-0.01050.1173-0.00280.0045-00.1461-0.01040.03270.142-0.01810.2401160.519887.36913.8963
570.0095-0.0104-0.00060.007600.00610.01730.01720.02260.0072-0.041-0.0516-0.0261-0.028400.1715-0.04060.02880.2082-0.02260.243175.032987.32886.7808
580.0072-0.0117-0.00350.01440.00460.00360.0440.06020.09280.0768-0.01510.04650.01690.0736-00.2045-0.00150.05080.1436-0.01370.2405167.758695.753617.0578
590.0085-0.00360.00520.0030.00320.00640.0827-0.05710.06680.1638-0.00590.0512-0.03870.00550.00440.2801-0.0120.08980.1833-0.04180.1694163.035986.213931.2749
600.1264-0.05090.05450.05330.0120.06480.11070.0009-0.02490.19450.06120.1849-0.0212-0.01690.06550.2123-0.02260.13690.1048-0.01850.1867159.72287.165924.1354
610.00970.0021-0.00070.0021-0.0010.00050.02780.0221-0.0016-0.0148-0.0195-0.10380.07280.0034-00.15040.0313-0.00670.12250.01190.1553131.169884.552118.1508
620.0115-0.01350.00410.011-0.00650.00390.07790.0141-0.0394-0.026-0.04130.0430.0817-0.0646-00.17460.04210.00140.17860.0130.1337117.299882.139410.1386
630.02-0.01840.00120.0074-0.00350.0140.10910.0218-0.17940.0239-0.0603-0.00850.0131-0.0002-0.00690.20880.0067-0.04980.1064-0.00380.133123.69676.132121.5974
640.03630.023-0.00160.0596-0.0070.01430.015-0.057-0.04950.1344-0.0746-0.04440.0458-0.0758-0.03710.23460.0593-0.07650.2067-0.01810.0459126.388487.9234.6067
650.1171-0.07270.00570.04680.02040.01540.0666-0.00120.04970.1218-0.0536-0.12520.13590.01370.01920.20110.0043-0.0630.13790.00390.1285130.391586.254928.3608
660.0032-0.00730.0010.0146-0.00560.0117-0.01060.01270.01960.0296-0.01310.05290.0071-0.0533-0.00150.14470.0181-0.03960.1812-0.02780.1389141.420152.828756.1969
670.00750.00940.00350.01-0.00020.00770.0426-0.0426-0.01230.0725-0.0193-0.0262-0.021-0.02530.00020.1590.0316-0.05140.1854-0.04510.1369154.937352.426764.7727
680.00510.00670.0050.00650.0050.00540.041-0.0725-0.0529-0.01380.00230.0136-0.01480.0052-00.24150.026-0.09620.1817-0.01370.1803151.17243.45754.3746
690.0219-0.01640.02370.0234-0.02870.0470.06970.0265-0.0448-0.110.00230.0410.03450.0570.06750.23340.0762-0.12220.2016-0.04650.0389146.113553.127646.137
700.04310.01010.00970.0225-0.00820.01430.0293-0.07420.0052-0.11380.00330.07520.03-0.06960.03890.21830.0562-0.09070.1548-0.02810.0721142.762355.791244.4515
710.0071-0.0078-0.00760.01080.00950.00410.0286-0.00340.0189-0.0045-0.06020.02010.0481-0.1439-0.00130.1181-0.0447-0.01190.2154-0.03820.1681142.0979114.664456.9373
720.02690.0235-0.01360.0176-0.0120.01650.0806-0.0676-0.1001-0.0035-0.0343-0.04610.0896-0.0791-0.00840.1774-0.0076-0.04990.2351-0.07010.1795156.0293114.130664.4036
730.00410.00480.00370.02130.00290.01890.1619-0.0331-0.14910.0615-0.09440.05310.03360.00920.00110.20540.0065-0.07580.1527-0.02780.1794149.3504106.720753.1483
740.00620.0041-0.00590.02710.00340.01440.05740.0478-0.017-0.1304-0.06610.04810.00120.0560.0020.19650.0614-0.08440.19-0.05340.0947145.3655117.973740.8671
750.07480.05010.03420.04180.00820.04750.0448-0.08650.0208-0.0719-0.13590.1209-0.0323-0.1261-0.02340.16110.0341-0.07330.1828-0.05340.1925142.8382117.298246.0121
760.002-0.00450.00080.01350.00850.02690.03220.02040.0275-0.0447-0.0516-0.131-0.04170.0134-0.00710.16860.03240.04110.135-0.01080.21111.975357.465760.0357
770.01010.00520.00270.00420.00670.0111-0.03350.02930.0198-0.061-0.03420.0278-0.0474-0.0166-00.17720.04460.02580.1584-0.00490.187897.224256.777666.4359
780.0050.006-0.00270.0154-0.00410.0136-0.0130.02090.1129-0.12190.0108-0.0046-0.01340.0443-0.00070.23560.03170.03040.1249-0.0050.1685105.30865.234556.8759
790.0046-0.00310.00560.00870.00170.00620.0360.03030.0619-0.1017-0.0297-0.0605-0.0332-0.0292-00.29530.05790.04270.2462-0.00410.1953110.494255.483644.7381
800.04040.00020.00830.0115-0.00580.02420.03390.0671-0.0129-0.1674-0.0511-0.0701-0.07080.0135-0.01630.21440.04210.06860.1446-0.00380.1529112.772156.10949.2056
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:18)
2X-RAY DIFFRACTION2(chain A and resid 19:94)
3X-RAY DIFFRACTION3(chain A and resid 95:199)
4X-RAY DIFFRACTION4(chain A and resid 200:232)
5X-RAY DIFFRACTION5(chain A and resid 233:246)
6X-RAY DIFFRACTION6(chain B and resid 0:19)
7X-RAY DIFFRACTION7(chain B and resid 20:35)
8X-RAY DIFFRACTION8(chain B and resid 36:100)
9X-RAY DIFFRACTION9(chain B and resid 101:219)
10X-RAY DIFFRACTION10(chain B and resid 220:246)
11X-RAY DIFFRACTION11(chain C and resid 0:20)
12X-RAY DIFFRACTION12(chain C and resid 21:124)
13X-RAY DIFFRACTION13(chain C and resid 125:219)
14X-RAY DIFFRACTION14(chain C and resid 220:239)
15X-RAY DIFFRACTION15(chain C and resid 240:246)
16X-RAY DIFFRACTION16(chain D and resid 0:18)
17X-RAY DIFFRACTION17(chain D and resid 19:108)
18X-RAY DIFFRACTION18(chain D and resid 109:183)
19X-RAY DIFFRACTION19(chain D and resid 184:233)
20X-RAY DIFFRACTION20(chain D and resid 234:246)
21X-RAY DIFFRACTION21(chain E and resid 0:76)
22X-RAY DIFFRACTION22(chain E and resid 77:88)
23X-RAY DIFFRACTION23(chain E and resid 89:124)
24X-RAY DIFFRACTION24(chain E and resid 125:219)
25X-RAY DIFFRACTION25(chain E and resid 220:246)
26X-RAY DIFFRACTION26(chain F and resid 0:6)
27X-RAY DIFFRACTION27(chain F and resid 7:18)
28X-RAY DIFFRACTION28(chain F and resid 19:149)
29X-RAY DIFFRACTION29(chain F and resid 150:219)
30X-RAY DIFFRACTION30(chain F and resid 220:246)
31X-RAY DIFFRACTION31(chain G and resid 0:18)
32X-RAY DIFFRACTION32(chain G and resid 19:147)
33X-RAY DIFFRACTION33(chain G and resid 148:196)
34X-RAY DIFFRACTION34(chain G and resid 197:219)
35X-RAY DIFFRACTION35(chain G and resid 220:247)
36X-RAY DIFFRACTION36(chain H and resid 0:10)
37X-RAY DIFFRACTION37(chain H and resid 11:48)
38X-RAY DIFFRACTION38(chain H and resid 49:149)
39X-RAY DIFFRACTION39(chain H and resid 150:219)
40X-RAY DIFFRACTION40(chain H and resid 220:246)
41X-RAY DIFFRACTION41(chain a and resid 1:33)
42X-RAY DIFFRACTION42(chain a and resid 34:66)
43X-RAY DIFFRACTION43(chain a and resid 67:118)
44X-RAY DIFFRACTION44(chain a and resid 119:149)
45X-RAY DIFFRACTION45(chain a and resid 150:228)
46X-RAY DIFFRACTION46(chain b and resid 2:32)
47X-RAY DIFFRACTION47(chain b and resid 33:66)
48X-RAY DIFFRACTION48(chain b and resid 67:116)
49X-RAY DIFFRACTION49(chain b and resid 117:149)
50X-RAY DIFFRACTION50(chain b and resid 150:228)
51X-RAY DIFFRACTION51(chain c and resid 3:34)
52X-RAY DIFFRACTION52(chain c and resid 35:66)
53X-RAY DIFFRACTION53(chain c and resid 67:116)
54X-RAY DIFFRACTION54(chain c and resid 117:155)
55X-RAY DIFFRACTION55(chain c and resid 156:226)
56X-RAY DIFFRACTION56(chain d and resid 1:33)
57X-RAY DIFFRACTION57(chain d and resid 34:66)
58X-RAY DIFFRACTION58(chain d and resid 67:118)
59X-RAY DIFFRACTION59(chain d and resid 119:155)
60X-RAY DIFFRACTION60(chain d and resid 156:228)
61X-RAY DIFFRACTION61(chain e and resid 1:34)
62X-RAY DIFFRACTION62(chain e and resid 35:67)
63X-RAY DIFFRACTION63(chain e and resid 68:117)
64X-RAY DIFFRACTION64(chain e and resid 118:155)
65X-RAY DIFFRACTION65(chain e and resid 156:227)
66X-RAY DIFFRACTION66(chain f and resid 1:31)
67X-RAY DIFFRACTION67(chain f and resid 32:66)
68X-RAY DIFFRACTION68(chain f and resid 67:95)
69X-RAY DIFFRACTION69(chain f and resid 96:146)
70X-RAY DIFFRACTION70(chain f and resid 147:226)
71X-RAY DIFFRACTION71(chain g and resid 1:31)
72X-RAY DIFFRACTION72(chain g and resid 32:66)
73X-RAY DIFFRACTION73(chain g and resid 67:117)
74X-RAY DIFFRACTION74(chain g and resid 118:153)
75X-RAY DIFFRACTION75(chain g and resid 154:225)
76X-RAY DIFFRACTION76(chain h and resid 0:31)
77X-RAY DIFFRACTION77(chain h and resid 32:66)
78X-RAY DIFFRACTION78(chain h and resid 67:118)
79X-RAY DIFFRACTION79(chain h and resid 119:149)
80X-RAY DIFFRACTION80(chain h and resid 150:228)

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月:コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか? / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例:em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る